MutationalPatterns      MutationalPatterns: an integrative R package
                        for studying patterns in base substitution
                        catalogues
binomial_test           Binomial test for enrichment or depletion
                        testing
enrichment_depletion_test
                        Test for enrichment or depletion of mutations
                        in genomic regions
extract_signatures      Extract mutational signatures from 96 mutation
                        matrix using NMF
fit_to_signatures       Find optimal nonnegative linear combination of
                        mutation signatures to reconstruct the mutation
                        matrix.
genomic_distribution    Find overlaps between mutations and a genomic
                        region.
mut_matrix              Make mutation count matrix of 96 trinucleotides
mut_matrix_stranded     Make mutation count matrix of 96 trinucleotides
                        with transcriptional strand information
mut_type_occurrences    Count the occurrences of each base substitution
                        type
mutation_context        Retrieve context of base substitutions
mutation_types          Retrieve base substitution types from a VCF
                        object
mutations_from_vcf      Retrieve base substitutions from vcf
plot_192_profile        Plot 192 trinucleotide profile
plot_96_profile         Plot 96 trinucleotide profile
plot_compare_profiles   Compare two 96 mutation profiles
plot_contribution       Plot signature contribution
plot_enrichment_depletion
                        Plot enrichment/depletion of mutations in
                        genomic regions
plot_rainfall           Plot genomic rainfall
plot_signature_strand_bias
                        Plot signature strand bias
plot_spectrum           Plot point mutation spectrum
plot_strand             Plot strand per base substitution type
plot_strand_bias        Plot strand bias per base substitution type
read_vcfs_as_granges    Read VCF files into a GRangesList
strand_bias_test        Significance test for transcriptional strand
                        asymmetry
strand_from_vcf         Find transcriptional strand of base
                        substitutions in vcf
strand_occurrences      Count occurrences per base substitution type
                        and transcriptional strand
type_context            Retrieve context of base substitution types
